Goal: track Alpha Diversity and Proportionality over samples and establish sample ordering
# devtools::install_github("tpq/propr")
Warning messages:
1: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
2: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
3: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
4: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
5: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
6: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
7: In if (charToRaw(x) < 20) paste("\\u", toupper(format(as.hexmode(as.integer(charToRaw(x))), :
the condition has length > 1 and only the first element will be used
# install.packages('ggdendro')
# devtools::install_github("jrnold/ggthemes")
# install.packages("ggthemes") # has tableau_tableau20 color palette
library("ggplot2"); packageVersion("ggplot2") # plotting
[1] ‘3.3.5’
library("tidyverse"); packageVersion("tidyverse") # util
Registered S3 methods overwritten by 'dbplyr':
method from
print.tbl_lazy
print.tbl_sql
── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✓ tibble 3.1.6 ✓ dplyr 1.0.7
✓ tidyr 1.1.4 ✓ stringr 1.4.0
✓ readr 2.1.1 ✓ forcats 0.5.1
✓ purrr 0.3.4
── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
x purrr::simplify() masks propr::simplify()
[1] ‘1.3.1’
library("dplyr"); packageVersion("dplyr") # util
[1] ‘1.0.7’
library("phyloseq"); packageVersion("phyloseq") # data object
[1] ‘1.38.0’
library("propr"); packageVersion("propr") # proportionality: compositional correlation
[1] ‘4.3.0’
# ggplot2 package theme set
theme_set(theme_bw())
# control randomization
set.seed(42)
# save outputs
save_location = "../data/processed_carbon_53OTUs/"
# color - days
color_day = c(
"3" = "#B2E5EA", # lightest
"5" = "#00BAE7",
"7" = "#0E6FA0",
"10" = "#012652",
"20" = "#01091C"
)
# color - growth.phase
color_growth.phase = c(
"early" = "black",
"mid C:C" = "springgreen3",
"late C:C" = "springgreen4",
"perturbed G" = "steelblue1",
"mid G:C" = "steelblue3",
"late G:C" = "steelblue4",
"perturbed M" = "sienna1",
"mid M:C" = "sienna3",
"late M:C" = "sienna4"
)
# shape - series
shape_series = c(
"C0C" = 4,
"C" = 16,
"G" = 15,
"M" = 17
)
# shape - carbon
shape_carbon = c(
"original" = 4,
"cellulose" = 16,
"glucose" = 18,
"malate" = 15
)
# shape - transfer
shape_transfer = c(
"C0C" = 4,
"1C" = 10,
"2C" = 16,
"1G" = 0,
"2G" = 12,
"3G" = 15,
"1M" = 5,
"2M" = 9,
"3M" = 18
)
# shape - growth phase
shape_growth.phase = c(
"early" = 1,
"mid C:C" = 16,
"late C:C" = 16,
"perturbed G" = 15,
"mid G:C" = 15,
"late G:C" = 15,
"perturbed M" = 17,
"mid M:C" = 17,
"late M:C" = 17
)
# color - genus
# for 20 color palette
tableau_20_colors <- ggthemes::ggthemes_data[["tableau"]][["color-palettes"]][["regular"]][["Tableau 20"]]$value
ps <- readRDS(paste(save_location, "phyloseq.rds", sep=""))
ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 53 taxa and 86 samples ]
sample_data() Sample Data: [ 86 samples by 11 sample variables ]
tax_table() Taxonomy Table: [ 53 taxa by 7 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 53 tips and 52 internal nodes ]
sample_data(ps)
Sample Data: [86 samples by 11 sample variables]:
sample_meta <- data.frame(sample_data(ps))
sample_meta
# make C0C part of C series
sample_meta$series[1] <- "C"
# make variable to store each time point (tp)
sample_meta <- sample_meta %>%
mutate(tp = paste(series, numerical_transfer, sprintf("%02d", numerical_day), sep="-"))
# reorder data frame
sample_meta <- sample_meta[with(sample_meta, order(series, numerical_transfer, numerical_day)),]
# make tp an ordered factor
sample_meta$tp <- factor(sample_meta$tp, levels = unique(sample_meta$tp))
# make variable to store tp_order (as numeric value)
tp_order_map <- 1:length(unique(sample_meta$tp))
names(tp_order_map) <- unique(sample_meta$tp)
sample_meta <- sample_meta %>%
mutate(tp_order = tp_order_map[as.character(tp)])
# final sample_meta
sample_meta
ggplot(sample_meta, aes(x=RC, y=shdiv, colour=growth.phase)) +
geom_point() +
geom_vline(xintercept = 70000, linetype = "dotted") +
geom_vline(xintercept = 120000, linetype = "dotted") +
scale_color_manual(values=color_growth.phase) +
theme_set(theme_classic()) +
ggtitle("RC vs. ShDiv")
ggplot(sample_meta, aes(x=RC, y=shdiv, alpha=0.3)) +
geom_point(show.legend = FALSE) +
geom_vline(xintercept = 70000, linetype = "dotted") +
geom_vline(xintercept = 120000, linetype = "dotted") +
theme_set(theme_classic()) +
ggtitle("RC vs. ShDiv")
ggplot(sample_meta, aes(x=RC, y="", alpha=0.3)) +
geom_jitter(show.legend = FALSE, width = 0) +
theme_set(theme_classic()) +
ggtitle("jitter (example of no correlation)")
sample_meta$tp
[1] C-0-10 C-1-03 C-1-03 C-1-05 C-1-05 C-1-07 C-1-07 C-1-10 C-1-10 C-1-20 C-1-20 C-2-03 C-2-03 C-2-05 C-2-05 C-2-10 C-2-10 G-1-03 G-1-03 G-1-03 G-1-05 G-1-05 G-1-05 G-1-07 G-1-07 G-1-07 G-1-10 G-1-10 G-1-10 G-2-03 G-2-03 G-2-03 G-2-05 G-2-05 G-2-05 G-2-07 G-2-07 G-2-07 G-2-10 G-2-10 G-2-10
[42] G-3-03 G-3-03 G-3-03 G-3-05 G-3-05 G-3-05 G-3-07 G-3-07 G-3-07 G-3-10 G-3-10 M-1-03 M-1-03 M-1-03 M-1-05 M-1-05 M-1-05 M-1-07 M-1-07 M-1-07 M-1-10 M-1-10 M-1-10 M-2-03 M-2-03 M-2-03 M-2-05 M-2-05 M-2-07 M-2-07 M-2-10 M-2-10 M-2-10 M-3-03 M-3-03 M-3-03 M-3-05 M-3-05 M-3-05 M-3-07 M-3-07
[83] M-3-07 M-3-10 M-3-10 M-3-10
Levels: C-0-10 C-1-03 C-1-05 C-1-07 C-1-10 C-1-20 C-2-03 C-2-05 C-2-10 G-1-03 G-1-05 G-1-07 G-1-10 G-2-03 G-2-05 G-2-07 G-2-10 G-3-03 G-3-05 G-3-07 G-3-10 M-1-03 M-1-05 M-1-07 M-1-10 M-2-03 M-2-05 M-2-07 M-2-10 M-3-03 M-3-05 M-3-07 M-3-10
sample_meta %>%
ggplot(aes(x=tp_order, y=shdiv)) +
geom_smooth(method = "loess", se = FALSE, colour="red") +
# geom_smooth(method = lm, se = FALSE, linetype = "dashed") +
geom_vline(xintercept = 2, linetype = "dotted") +
geom_vline(xintercept = 7, linetype = "dotted") +
geom_vline(xintercept = 10, linetype = "dotted") +
geom_vline(xintercept = 14, linetype = "dotted") +
geom_vline(xintercept = 18, linetype = "dotted") +
geom_vline(xintercept = 22, linetype = "dotted") +
geom_vline(xintercept = 26, linetype = "dotted") +
geom_vline(xintercept = 30, linetype = "dotted") +
geom_point(aes(x=tp_order, y=shdiv, colour=growth.phase)) +
scale_color_manual(values=color_growth.phase) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_x_discrete(name = "time points",
limits=unique(sample_meta$tp)) +
ggtitle("all")
`geom_smooth()` using formula 'y ~ x'
sample_meta %>%
filter(RC > 70000 & RC < 120000) %>%
ggplot(aes(x=tp_order, y=shdiv)) +
geom_smooth(method = "loess", se = FALSE, colour="red") +
# geom_smooth(method = lm, se = FALSE, linetype = "dashed") +
geom_vline(xintercept = 2, linetype = "dotted") +
geom_vline(xintercept = 7, linetype = "dotted") +
geom_vline(xintercept = 10, linetype = "dotted") +
geom_vline(xintercept = 14, linetype = "dotted") +
geom_vline(xintercept = 18, linetype = "dotted") +
geom_vline(xintercept = 22, linetype = "dotted") +
geom_vline(xintercept = 26, linetype = "dotted") +
geom_vline(xintercept = 30, linetype = "dotted") +
geom_point(aes(x=tp_order, y=shdiv, colour=growth.phase)) +
scale_color_manual(values=color_growth.phase) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_x_discrete(name = "time points",
limits=unique(sample_meta$tp)) +
ggtitle("mid-band")
`geom_smooth()` using formula 'y ~ x'
# # only do correlation on cellulose samples --> no we want to capture corr. when perturbed and recover because overall it is same
# ps_cellulose <- readRDS(paste(save_location, "phyloseq_cellulose.rds", sep=""))
# ps_cellulose_clr <- microbiome::transform(ps_cellulose, "clr")
ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 53 taxa and 86 samples ]
sample_data() Sample Data: [ 86 samples by 11 sample variables ]
tax_table() Taxonomy Table: [ 53 taxa by 7 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 53 tips and 52 internal nodes ]
(ps_clr <- microbiome::transform(ps, "clr"))
phyloseq-class experiment-level object
otu_table() OTU Table: [ 53 taxa and 86 samples ]
sample_data() Sample Data: [ 86 samples by 11 sample variables ]
tax_table() Taxonomy Table: [ 53 taxa by 7 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 53 tips and 52 internal nodes ]
counts <- t(as(otu_table(ps), "matrix"))
(pr <- propr(counts, # rows as samples, like it should be
metric = "rho", # or "phi", "phs", "cor", "vlr"
ivar = "clr", # or can use "iqlr" instead
alpha = NA, # use to handle zeros
p = 100)) # used by updateCutoffs
Alert: Replacing 0s with next smallest value.
Alert: Saving log-ratio transformed counts to @logratio.
Alert: Fixing permutations to active random seed.
Alert: Tabulating the presence of 0 counts.
Alert: Use '[' to index proportionality matrix.
Alert: Use 'updateCutoffs' to calculate FDR.
Not weighted and not alpha-transformed
@counts summary: 86 subjects by 53 features
@logratio summary: 86 subjects by 53 features
@matrix summary: 53 features by 53 features
@pairs summary: index with `[` method
@fdr summary: iterations
See ?propr for object methods
# Choose the largest cutoff with an acceptable FDR.
updateCutoffs(pr,
cutoff = seq(0, 1, .05), # cutoffs at which to estimate FDR
ncores = 1) # parallelize here
Alert: Try parallelizing updateCutoffs with ncores > 1.
Alert: Estimating FDR for largely positive proportional pairs only.
|------------(25%)----------(50%)----------(75%)----------|
Not weighted and not alpha-transformed
@counts summary: 86 subjects by 53 features
@logratio summary: 86 subjects by 53 features
@matrix summary: 53 features by 53 features
@pairs summary: index with `[` method
@fdr summary: iterations
See ?propr for object methods
# narrow down range to find FDR ~0.05
updateCutoffs(pr,
cutoff = seq(0.25, 0.30, .01), # cutoffs at which to estimate FDR
ncores = 1) # parallelize here
Alert: Try parallelizing updateCutoffs with ncores > 1.
Alert: Estimating FDR for largely positive proportional pairs only.
|------------(25%)----------(50%)----------(75%)----------|
Not weighted and not alpha-transformed
@counts summary: 86 subjects by 53 features
@logratio summary: 86 subjects by 53 features
@matrix summary: 53 features by 53 features
@pairs summary: index with `[` method
@fdr summary: iterations
See ?propr for object methods
# Parameters
CUTOFF = 0.29 # rho cutoff
N <- 12 # number of clusters
# subsetting propr object to the @pairs slot
pr_best <- pr[">", CUTOFF]
pr_best@pairs
[1] 2 3 4 5 6 7 8 9 30 41 51 56 57 58 59 60 61 62 64 65 68 69 77 89 90 92 110 111 112 113 114 121 130 164 165 166 167 174 183 189 200 218 219 220 227 236 272 354 380 382 383 386 387 395 435 436 439
[58] 440 448 457 459 460 461 488 489 508 542 547 561 565 566 567 598 600 614 618 619 620 650 661 662 663 706 714 715 716 720 724 726 741 758 759 766 781 813 814 815 816 818 819 827 834 872 874 875 879 883 884 885 920 921 922 923 924
[115] 931 933 939 940 942 952 974 975 976 977 984 986 992 993 995 1005 1028 1029 1030 1037 1039 1045 1046 1048 1082 1083 1090 1092 1098 1099 1101 1111 1136 1145 1151 1152 1196 1198 1204 1205 1207 1217 1258 1298 1299 1352 1356 1460 1462 1473 1474 1476 1477 1480 1481 1483 1484
[172] 1515 1526 1527 1529 1530 1531 1533 1534 1536 1537 1569 1575 1577 1578 1588 1626 1632 1633 1634 1635 1636 1637 1639 1640 1642 1643 1676 1681 1682 1684 1694 1730 1731 1732 1733 1798 1799 1838 1839 1840 1892 1946 2000 2108 2118 2171 2216 2217 2218 2219 2220 2221 2222 2223 2225 2226 2270
[229] 2271 2272 2273 2274 2276 2278 2279 2324 2325 2326 2327 2331 2332 2378 2379 2380 2381 2382 2384 2385 2432 2433 2434 2435 2437 2438 2486 2490 2491 2594 2595 2649 2650 2756
# pr_best <- simplify(pr_best)
Look at the prism and bokeh functions for visualizing the co-clustering of proportional features. These plots share some key similarities: * they are all “index-naive” * they identify the feature pairs where both constituents co-cluster (with the total number of clusters toggled by k). * they return a vector of cluster memberships for all features in the propr object.
The prism function plots the variance of the ratio of the log-ratio transformed feature pair (VLR) versus the sum of the individual variances of each log-ratio transformed feature (VLS). The ratio of the VLR to the VLS equals 1−ρ. As such, we use here seven rainbow colored lines to indicate where ρ=[.01, .05, .50, 0, 1.50, 1.95, 1.99], going from red to violet. A low VLR with a high VLS suggests that the feature pair remains in an equilibrium despite high variability among the individual features.
pr_prism <- propr::prism(pr, k = N)
Warning in RColorBrewer::brewer.pal(n, pal) :
n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors
Warning: Removed 54 rows containing missing values (geom_point).
The bokeh function plots pairs across the individual variances of the constituent log-ratio transformed features. For clarity of visualization, this figure projects the data on a log-fold scale. Therefore, the highly variable co-clusters appear in the top-right of the figure while the lowly variable co-clusters appear in the bottom-left. Meanwhile, highly proportional pairs tend to aggregate around the y=x diagonal.
bokeh(pr, k = N)
Warning in RColorBrewer::brewer.pal(n, pal) :
n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors
Warning: Removed 54 rows containing missing values (geom_point).
OTU_640 OTU_23 OTU_3 OTU_107 OTU_298 OTU_87 OTU_437 OTU_27 OTU_14 OTU_429 OTU_5 OTU_136 OTU_25 OTU_215 OTU_4 OTU_548 OTU_41 OTU_467 OTU_67 OTU_608 OTU_222 OTU_315 OTU_6 OTU_259 OTU_9 OTU_521 OTU_569 OTU_116 OTU_11 OTU_43 OTU_16 OTU_284 OTU_7 OTU_20 OTU_409 OTU_565
1 1 2 2 2 2 2 1 1 3 3 3 4 4 5 5 6 7 7 7 7 8 7 5 4 4 4 9 9 10 10 7 11 11 6 6
OTU_2 OTU_115 OTU_484 OTU_15 OTU_22 OTU_457 OTU_10 OTU_51 OTU_274 OTU_211 OTU_224 OTU_36 OTU_13 OTU_30 OTU_12 OTU_584 OTU_8
6 8 8 10 10 12 12 12 7 12 12 12 9 9 10 7 7
unique(pr_prism)
[1] 1 2 3 4 5 6 7 8 9 10 11 12
# save
write.csv(df_c, paste(save_location, "propr.csv", sep=""), quote = FALSE)
df_c_longer <- df_c %>%
# pivot data so each row has x=sampleID, y=clr
pivot_longer(phyloseq::sample_names(ps_clr),
names_to = "sampleID",
values_to = "clr") %>%
# add variable series
mutate(series = sample_meta[sampleID, "series"]) %>%
# add variable growth.phase
mutate(growth.phase = sample_meta[sampleID, "growth.phase"]) %>%
# add variable tp
mutate(tp = sample_meta[sampleID, "tp"]) %>%
# add variable tp_order
mutate(tp_order = sample_meta[sampleID, "tp_order"])
# establish that tp is an ordered factor
df_c_longer$tp <- factor(df_c_longer$tp, levels = unique(sample_meta$tp))
# reorder data frame
df_c_longer <- df_c_longer[with(df_c_longer, order(tp)),]
df_c_longer
# line plot, faceted by cluster, colored by taxrank
df_c_longer %>%
ggplot(aes(x=tp, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_line() +
geom_vline(xintercept = "C-1-03", linetype = "dotted") +
geom_vline(xintercept = "C-2-03", linetype = "dotted") +
geom_vline(xintercept = "G-1-03", linetype = "dotted") +
geom_vline(xintercept = "G-2-03", linetype = "dotted") +
geom_vline(xintercept = "G-3-03", linetype = "dotted") +
geom_vline(xintercept = "M-1-03", linetype = "dotted") +
geom_vline(xintercept = "M-2-03", linetype = "dotted") +
geom_vline(xintercept = "M-3-03", linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
ggtitle("all") +
facet_wrap( ~ cluster)
# line plot, faceted by cluster, colored by taxrank
df_c_longer %>%
filter(series == "C") %>%
ggplot(aes(x=tp, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_line() +
geom_vline(xintercept = "C-1-03", linetype = "dotted") +
geom_vline(xintercept = "C-2-03", linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
ggtitle("cellulose series") +
facet_wrap( ~ cluster)
# line plot, faceted by cluster, colored by taxrank
df_c_longer %>%
filter(series == "G") %>%
ggplot(aes(x=tp, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_line() +
geom_vline(xintercept = "G-1-03", linetype = "dotted") +
geom_vline(xintercept = "G-2-03", linetype = "dotted") +
geom_vline(xintercept = "G-3-03", linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
ggtitle("glucose series") +
facet_wrap( ~ cluster)
# line plot, faceted by cluster, colored by taxrank
df_c_longer %>%
filter(series == "M") %>%
ggplot(aes(x=tp, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_line() +
geom_vline(xintercept = "M-1-03", linetype = "dotted") +
geom_vline(xintercept = "M-2-03", linetype = "dotted") +
geom_vline(xintercept = "M-3-03", linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
ggtitle("malate series") +
facet_wrap( ~ cluster)
tp_order_map
C-0-10 C-1-03 C-1-05 C-1-07 C-1-10 C-1-20 C-2-03 C-2-05 C-2-10 G-1-03 G-1-05 G-1-07 G-1-10 G-2-03 G-2-05 G-2-07 G-2-10 G-3-03 G-3-05 G-3-07 G-3-10 M-1-03 M-1-05 M-1-07 M-1-10 M-2-03 M-2-05 M-2-07 M-2-10 M-3-03 M-3-05 M-3-07 M-3-10
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33
color_growth.phase
early mid C:C late C:C perturbed G mid G:C late G:C perturbed M mid M:C late M:C
"black" "springgreen3" "springgreen4" "steelblue1" "steelblue3" "steelblue4" "sienna1" "sienna3" "sienna4"
df_c_longer %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE, lwd=2.0) +
# geom_point(alpha = 0.3) +
geom_vline(xintercept = 2, linetype = "solid", colour=color_growth.phase["mid C:C"]) +
geom_vline(xintercept = 7, linetype = "dotted") +
geom_vline(xintercept = 10, linetype = "solid", colour=color_growth.phase["perturbed G"]) +
geom_vline(xintercept = 14, linetype = "dotted") +
geom_vline(xintercept = 18, linetype = "dotted") +
geom_vline(xintercept = 22, linetype = "solid", colour=color_growth.phase["perturbed M"]) +
geom_vline(xintercept = 26, linetype = "dotted") +
geom_vline(xintercept = 30, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=1)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB",
limits = c(-7, 7),
breaks=c(-5, 0, 5)
) +
scale_x_discrete(name = "time points",
limits=unique(df_c_longer$tp)) +
ggtitle("all") +
facet_wrap( ~ cluster)
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 11 rows containing non-finite values (stat_smooth).
df_c_longer %>%
filter(series == "C") %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 2, linetype = "solid", colour=color_growth.phase["mid C:C"]) +
geom_vline(xintercept = 7, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB",
limits = c(-7, 7),
breaks=c(-5, 0, 5)
) +
scale_x_discrete(name = "time points",
limits=1:10,
labels=names(tp_order_map)[1:10]) +
ggtitle("cellulose series") +
facet_wrap( ~ cluster)
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
df_c_longer %>%
filter(series == "G") %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 10, linetype = "dotted") +
geom_vline(xintercept = 14, linetype = "solid", colour=color_growth.phase["mid C:C"]) +
geom_vline(xintercept = 18, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB",
limits = c(-7, 7),
breaks=c(-5, 0, 5)
) +
scale_x_discrete(name = "time points",
limits=11:21,
labels=names(tp_order_map)[11:21]) +
ggtitle("glucose series") +
facet_wrap( ~ cluster)
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_smooth).
df_c_longer %>%
filter(series == "M") %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 22, linetype = "dotted") +
geom_vline(xintercept = 26, linetype = "solid", colour=color_growth.phase["mid C:C"]) +
geom_vline(xintercept = 30, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB",
limits = c(-7, 7),
breaks=c(-5, 0, 5)
) +
scale_x_discrete(name = "time points",
limits=22:33,
labels=names(tp_order_map)[22:33]) +
ggtitle("malate series") +
facet_wrap( ~ cluster)
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 9 rows containing non-finite values (stat_smooth).
df_c_longer %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=family), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 2, linetype = "dotted") +
geom_vline(xintercept = 7, linetype = "dotted") +
geom_vline(xintercept = 10, linetype = "dotted") +
geom_vline(xintercept = 14, linetype = "dotted") +
geom_vline(xintercept = 18, linetype = "dotted") +
geom_vline(xintercept = 22, linetype = "dotted") +
geom_vline(xintercept = 26, linetype = "dotted") +
geom_vline(xintercept = 30, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB", breaks=c(0, 5, 10)) +
scale_x_discrete(name = "time points",
limits=unique(df_c_longer$tp)) +
ggtitle("all") +
facet_wrap( ~ cluster)
`geom_smooth()` using formula 'y ~ x'
df_c_longer %>%
filter(series == "C") %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=family), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 2, linetype = "dotted") +
geom_vline(xintercept = 7, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB", breaks=c(0, 5, 10)) +
scale_x_discrete(name = "time points",
limits=1:10,
labels=names(tp_order_map)[1:10]) +
ggtitle("cellulose series") +
facet_wrap( ~ cluster)
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
df_c_longer %>%
filter(series == "G") %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=family), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 10, linetype = "dotted") +
geom_vline(xintercept = 14, linetype = "dotted") +
geom_vline(xintercept = 18, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB", breaks=c(0, 5, 10)) +
scale_x_discrete(name = "time points",
limits=11:21,
labels=names(tp_order_map)[11:21]) +
ggtitle("glucose series") +
facet_wrap( ~ cluster)
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
df_c_longer %>%
filter(series == "M") %>%
ggplot(aes(x=tp_order, y=clr, group=OTU, color=family), alpha=0.3) +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 22, linetype = "dotted") +
geom_vline(xintercept = 26, linetype = "dotted") +
geom_vline(xintercept = 30, linetype = "dotted") +
scale_colour_manual(values = tableau_20_colors) +
guides(color=guide_legend(ncol=2)) +
theme_set(theme_classic()) +
theme(axis.text.x = element_text(angle = 60, hjust = 1)) +
scale_y_continuous(name = "log2 rAB", breaks=c(0, 5, 10)) +
scale_x_discrete(name = "time points",
limits=22:33,
labels=names(tp_order_map)[22:33]) +
ggtitle("malate series") +
facet_wrap( ~ cluster)
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
Plots: A: C0C - C1 B: C1-20 - C1
C: C0C - G1 D: G1-10 - G2 E: G2-10 - G3
F: C0C - M1 G: M1-10 - M2 H: M2-10 - M3
unique(sample_meta$tp)
[1] C-0-10 C-1-03 C-1-05 C-1-07 C-1-10 C-1-20 C-2-03 C-2-05 C-2-10 G-1-03 G-1-05 G-1-07 G-1-10 G-2-03 G-2-05 G-2-07 G-2-10 G-3-03 G-3-05 G-3-07 G-3-10 M-1-03 M-1-05 M-1-07 M-1-10 M-2-03 M-2-05 M-2-07 M-2-10 M-3-03 M-3-05 M-3-07 M-3-10
Levels: C-0-10 C-1-03 C-1-05 C-1-07 C-1-10 C-1-20 C-2-03 C-2-05 C-2-10 G-1-03 G-1-05 G-1-07 G-1-10 G-2-03 G-2-05 G-2-07 G-2-10 G-3-03 G-3-05 G-3-07 G-3-10 M-1-03 M-1-05 M-1-07 M-1-10 M-2-03 M-2-05 M-2-07 M-2-10 M-3-03 M-3-05 M-3-07 M-3-10
sample_meta$transfer
[1] C0C 1C 1C 1C 1C 1C 1C 1C 1C 1C 1C 2C 2C 2C 2C 2C 2C 1G 1G 1G 1G 1G 1G 1G 1G 1G 1G 1G 1G 2G 2G 2G 2G 2G 2G 2G 2G 2G 2G 2G 2G 3G 3G 3G 3G 3G 3G 3G 3G 3G 3G 3G 1M 1M 1M 1M 1M 1M 1M 1M 1M 1M 1M 1M 2M 2M 2M 2M 2M 2M 2M 2M
[73] 2M 2M 3M 3M 3M 3M 3M 3M 3M 3M 3M 3M 3M 3M
Levels: C0C 1C 2C 1G 2G 3G 1M 2M 3M
# new data frame
df_d_longer <- df_c %>%
# pivot data so each row has x=sampleID, y=clr
pivot_longer(phyloseq::sample_names(ps_clr),
names_to = "sampleID",
values_to = "clr") %>%
# add variable transfer
mutate(transfer = sample_meta[sampleID, "transfer"]) %>%
# add variable tp
mutate(tp = sample_meta[sampleID, "tp"])
# establish that tp is an ordered factor
df_d_longer$tp <- factor(df_d_longer$tp, levels = unique(sample_meta$tp))
# reorder data frame
df_d_longer <- df_d_longer[with(df_d_longer, order(tp)),]
df_d_longer
plot_corr_per_transfer <- function(df_d_longer, tp_order_map, title, legend_pos="right") {
df_d_longer %>%
# filter data
filter(tp %in% names(tp_order_map)) %>%
# numerical ordered x-axis
mutate(tp_order = tp_order_map[as.character(tp)]) %>%
# plot
ggplot(aes(x=tp_order, y=clr, group=OTU, color=genus), alpha=0.3) +
geom_point() +
geom_smooth(method = "loess", se = FALSE) +
geom_vline(xintercept = 2, linetype = "dotted", alpha=0.3) +
geom_hline(yintercept = 5, linetype = "dotted", alpha=0.3) +
geom_hline(yintercept = 0, linetype = "dashed", alpha=0.3) +
geom_hline(yintercept = -5, linetype = "dotted", alpha=0.3) +
theme_set(theme_classic()) +
scale_colour_manual(values = tableau_20_colors) +
theme(axis.text.x = element_text(angle = 60, hjust = 1),
legend.position = legend_pos) +
guides(color=guide_legend(ncol=2)) +
scale_y_continuous(name = "log2 rAB",
limits = c(-7, 7),
breaks=c(-5, 0, 5)) +
# x-axis labeling
scale_x_discrete(name = "time points",
limits=1:length(tp_order_map),
labels=names(tp_order_map)) +
facet_wrap( ~ cluster) +
ggtitle(title)
}
unique(df_d_longer$tp)
[1] C-0-10 C-1-03 C-1-05 C-1-07 C-1-10 C-1-20 C-2-03 C-2-05 C-2-10 G-1-03 G-1-05 G-1-07 G-1-10 G-2-03 G-2-05 G-2-07 G-2-10 G-3-03 G-3-05 G-3-07 G-3-10 M-1-03 M-1-05 M-1-07 M-1-10 M-2-03 M-2-05 M-2-07 M-2-10 M-3-03 M-3-05 M-3-07 M-3-10
Levels: C-0-10 C-1-03 C-1-05 C-1-07 C-1-10 C-1-20 C-2-03 C-2-05 C-2-10 G-1-03 G-1-05 G-1-07 G-1-10 G-2-03 G-2-05 G-2-07 G-2-10 G-3-03 G-3-05 G-3-07 G-3-10 M-1-03 M-1-05 M-1-07 M-1-10 M-2-03 M-2-05 M-2-07 M-2-10 M-3-03 M-3-05 M-3-07 M-3-10
# 1C
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"C-0-10" = 1,
"C-1-03" = 2,
"C-1-05" = 3,
"C-1-07" = 4,
"C-1-10" = 5,
"C-1-20" = 6),
title = "first transfer onto cellulose (1C)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
# 2C
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"C-1-20" = 1,
"C-2-03" = 2,
"C-2-05" = 3,
"C-2-10" = 4),
title = "second transfer onto cellulose (2C)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.985
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.015
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 6.924e-17
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 4.0602
# 1G
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"C-0-10" = 1,
"G-1-03" = 2,
"G-1-05" = 3,
"G-1-07" = 4,
"G-1-10" = 5),
title = "perturbation transfer onto glucose (1G)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 2 rows containing non-finite values (stat_smooth).
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_smooth).
# 2G
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"G-1-10" = 1,
"G-2-03" = 2,
"G-2-05" = 3,
"G-2-07" = 4,
"G-2-10" = 5),
title = "first transfer back onto cellulose (2G)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
# 3G
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"G-2-10" = 1,
"G-3-03" = 2,
"G-3-05" = 3,
"G-3-07" = 4,
"G-3-10" = 5),
title = "second transfer back onto cellulose (3G)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
# 1M
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"C-0-10" = 1,
"M-1-03" = 2,
"M-1-05" = 3,
"M-1-07" = 4,
"M-1-10" = 5),
title = "perturbation transfer onto malate (1M)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
Warning: Removed 9 rows containing non-finite values (stat_smooth).
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
span too small. fewer data values than degrees of freedom.
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 0.98
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 4.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
radius 0.0004
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
all data on boundary of neighborhood. make span bigger
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 0.0004
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
zero-width neighborhood. make span bigger
Warning: Computation failed in `stat_smooth()`:
NA/NaN/Inf in foreign function call (arg 5)
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
pseudoinverse used at 5.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
neighborhood radius 2.02
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
reciprocal condition number 0
Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
There are other near singularities as well. 1
Warning: Removed 9 rows containing missing values (geom_point).
# 2M
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"M-1-10" = 1,
"M-2-03" = 2,
"M-2-05" = 3,
"M-2-07" = 4,
"M-2-10" = 5),
title = "first transfer back onto cellulose (2M)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'
# 3M
plot_corr_per_transfer(df_d_longer,
tp_order_map = c(
"M-2-10" = 1,
"M-3-03" = 2,
"M-3-05" = 3,
"M-3-07" = 4,
"M-3-10" = 5),
title = "second transfer back onto cellulose (3M)")
Warning: Continuous limits supplied to discrete scale.
Did you mean `limits = factor(...)` or `scale_*_continuous()`?
`geom_smooth()` using formula 'y ~ x'